HMM Logo

Representation of the per-position residue
and indel conservation of the HMM. Each position in the model is represented
by a stack of letters, with the stack height indicating the information content
of the position, and rate and expected length of insertions after each position
shown in the fields below each stack.

Genome Specific Characteristics

Non-Redundant Coverage, Conservation, and Inserts

Plot showing, for hits above a variety of thresholds, (1) the distribution
of hits along the model, (2) the
position-specific levels of conservation of those hits, and (3)
the position-specific rates of insertion among those hits.
For a selected threshold, the purple line shows, for each model
position, the fraction of all hits that have a match to that position,
considering only RPH-filtered hits (hits for which this model is
deemed to fit the sequence better than any other Dfam model).
Among RPH-filtered hits, the green
line shows, for each position, the average percent identity for a window
of length 7 around the position. The grey line shows the number of
insertions among those hits. In the threshold selection
box, the number in parentheses shows the number of hits meeting
the given threshold.

Fraction of hits covering each position of the model, and
per-position sequence identity and insertion rate based on those hits.

Non-Redundant Coverage

Plot showing the distribution across the model for all above-threshold hits, after removing redundant
profile hits (RPHs: hits to other Dfam profile HMMs that are deemed to be of higher quality than the corresponding hit to this model).

Number of aligned bases per model position, among the non-redundant
hits in dfamseq.

Redundant Coverage

Plot showing how all above-threshold matches to
dfamseq are distributed across the model. These hits may include many hits that are preferentially
hit by some other model.

Number of aligned bases per model position, using the hits in dfamseq.

False Coverage

Plot showing how matches to artificial non-TE sequence
are distributed across the model.

Number of aligned bases per model position, using the hits from an artificial sequence devoid of TEs.

Seed Coverage

Plot showing how sequences in the seed alignment are distributed across model positions.

Number of aligned bases per model position in the 294 deep seed alignment.

Seed Whisker Plot

More detailed view than above, showing one line for each seed alignment sequence, with line range
indicating the positions of the model corresponding to that sequence.

Representation of the 294 seed alignment sequences, indicating their length distribution
across the model.